Pressure of Linear and Ring Polymers Confined in a Cavity.

Nanoscale confinement of polymers in a cavity is central to a variety of biological and nanotechnology processes. Using the discrete WLC model we simulate the compression of flexible and semiflexible polymers of linear and ring topology in a closed cavity. Simulation reveals that polymer pressure inside the cavity increases with the chain stiffness but is practically unaffected by the chain topology.

Energy/entropy partition of force at DNA stretching.

We compute by molecular simulation the energy/entropic partition of the force in a stretched double-stranded (ds)DNA molecule that is not yet available from the single-molecule measurements. Simulation using the coarse-grained wormlike chain (WLC) model predicts a gradual decrease in the internal (bending) energy of DNA at stretching. The ensuing negative energy contribution to force f is outweighed by the positive entropy contribution f .

Conformation of Flexible and Semiflexible Chains Confined in Nanoposts Array of Various Geometries.

The conformation and distribution of a flexible and semiflexible chain confined in an array of nanoposts arranged in parallel way in a square-lattice projection of their cross-section was investigated using coarse-grained molecular dynamics simulations. The geometry of the nanopost array was varied at the constant post diameter and the ensuing modifications of the chain conformation were compared with the structural behavior of the chain in the series of nanopost arrays with the constant post separation as well as with the constant distance between two adjacent post walls (passage width) . The free energy arguments based on an approximation of the array of nanopost to a composite of quasi-channels of diameter and quasi-slits of height provide semiqualitative explanations for the observed structural behavior of both chains.

Compression and Stretching of Single DNA Molecules under Channel Confinement.

We study the compression and extension response of single dsDNA (double-stranded DNA) molecules confined in cylindrical channels by means of Monte Carlo simulations. The elastic response of micrometer-sized DNA to the external force acting through the chain ends or through the piston is markedly affected by the size of the channel. The interpretation of the force ()-displacement () functions under quasi-one-dimensional confinement is facilitated by resolving the overall change of displacement Δ into the confinement contribution Δ and the force contribution Δ.

Force-displacement relations at compression of dsDNA macromolecules.

The elasticity of dsDNA molecules is investigated by Monte Carlo simulations based on a coarse-grained model of DNA. The force-displacement (f-r) curves are computed under the constraints of the constant force (Gibbs) or the constant length (Helmholtz) ensemble. Particular attention was paid to the compressional (negative) and weak tensile forces.

Block Copolymer of Flexible and Semi-Flexible Block Confined in Nanopost Array.

Coarse-grained molecular dynamics simulations of a diblock copolymer consisting of a flexible and semi-flexible block in a dense array of parallel nanoposts with a square lattice packing were performed. The mutual interactions between the two blocks of the confined diblock chain were investigated through a comparison of their size, structure, and penetration among nanoposts with the corresponding separate chains. The geometry of a nanopost array was varied at constant post separation or at constant width of the passage between nanoposts.

Correlation anisotropy and stiffness of DNA molecules confined in nanochannels.

The anisotropy of orientational correlations in DNA molecules confined in cylindrical channels is explored by Monte Carlo simulations using a coarse-grained model of double-stranded (ds) DNA. We find that the correlation function ⟨C(s)⟩ in the transverse (confined) dimension exhibits a region of negative values in the whole range of channel sizes. Such a clear-cut sign of the opposite orientation of chain segments represents a microscopic validation of the Odijk deflection mechanism in narrow channels.

Stretching and compression of DNA by external forces under nanochannel confinement.

Mechanical deformation of dsDNA molecules inside square nanochannels is investigated using simulations based on a coarse-grained model of DNA. The combined action of confinement and weak external forces is explored in a variety of confinement regimes, including the transition zone relevant to nanofluidic experiments. The computed free energy and force profiles are markedly affected by the channel size.

Correction: Benková, Z.; et al. Structural Behavior of a Semiflexible Polymer Chain in an Array of Nanoposts 2017, , 313.

[This corrects the article DOI: 10.3390/polym9080313.].

Effect of chain stiffness for semiflexible macromolecules in array of cylindrical nanoposts.

Equilibrium conformation of a semiflexible macromolecule in an array of nanoposts exhibits a non-monotonic behavior both at variation of the chain stiffness and increased crowding imposed by nanoposts. This is a result of the competition between the axial chain extension in channel-like interstitial volumes between nanoposts and the chain partitioning among these volumes. The approximation of a nanopost array as a combination of a quasi-channel and a quasi-slit like geometry semi-qualitatively explains the behavior of a chain in the array.

Structural Behavior of a Semiflexible Polymer Chain in an Array of Nanoposts.

The structural properties of a flexible and semiflexible circular chain confined in an array of parallel nanoposts with a square lattice cross-sectional projection were studied using coarse-grained molecular dynamics simulations. To address the effect of the circular topology, a comparison with linear analogs was also carried out. In the interpretation of the chain structural properties, the geometry of the post array is considered as a combination of a channel approximating the interstitial volume with the diameter and a slit approximating the passage aperture with the width .

Comparison of a stripe and slab confinement for ring and linear macromolecules in nanochannel.

The combined effects of the channel asymmetry and the closed chain topology on the chain extension, structure factor, and the orientation correlations were studied using coarse-grained molecular dynamics simulations for moderate chain lengths. These effects are related to applications in linearization experiments with a DNA molecule in nanofluidic devices. According to the aspect ratio, the channels are classified as a stripe or slabs.

Arm retraction and escape transition in semi-flexible star polymer under cylindrical confinement.

We studied the structure and dynamics of star-shaped polymers by means of coarse-grained molecular dynamics simulations and analysis of structural transitions of semi-flexible macromolecules confined in nano-channels. The conformation of star arms in narrow channels is given by the channel width, arm flexibility and number of arms aligned together in the given region along the channel. We focused on the conformation transition, where all arms are initially stretched in one direction of the narrow channel and were interested in the process of how individual arms escape into a free volume region of channel.

Structural transformation between long and short-chain form of liquid sulfur from ab initio molecular dynamics.

We present results of ab initio molecular dynamics study of the structural transformation occurring in hot liquid sulfur under high pressure, which corresponds to the recently observed chain-breakage phenomenon and to the electronic transition reported earlier. The transformation is temperature-induced and separates two distinct polymeric forms of liquid sulfur: high-temperature form composed of short chain-like fragments with open endings and low-temperature form with very long chains. We offer a structural description of the two liquid forms in terms of chain lengths, cross-linking, and chain geometry and investigate several physical properties.

Stripe to slab confinement for the linearization of macromolecules in nanochannels.

We investigated the recently suggested advantageous analysis of chain linearization experiments with macromolecules confined in a stripe-like channel (Huang and Battacharya, EPL, 2014, 106, 18004) using Monte Carlo simulations. The enhanced chain extension in a stripe, which is due to the significant excluded volume interactions between the monomers in two dimensions, weakens considerably on transition to an experimentally feasible slit-like channel. Based on the chain extension-confinement strength dependence and the structure factor behavior for a chain in a stripe, we infer the excluded volume regime (de Gennes regime) typical for two-dimensional systems.

Segregation of semiflexible macromolecules in nanochannel.

Investigation of segregation of polymer coils in open channel was extended relative to previous studies from flexible chains to semiflexible chains. Our results are based on simulation of confinement free energy of a chain in channel and on direct simulation of coil segregation process. For confinement free energy, we confirm the predicted opposite trend with increasing chain stiffness for the weak and for strong confinement regimes.

Comparison of linear and ring DNA macromolecules moderately and strongly confined in nanochannels.

Understanding the mechanism of DNA extension in nanochannels is necessary for interpretation of experiments in nanofluidic channel devices that have been conducted recently with both linear and ring chains. The present article reviews the situation with linear chains and analyses the experimental results and simulations for channel-induced extension (linearization) of ring chains. Results for confined rings indicate a transition between moderate and strong confinement similar to that of linear chains.

Effective stiffening of DNA due to nematic ordering causes DNA molecules packed in phage capsids to preferentially form torus knots.

Observation that DNA molecules in bacteriophage capsids preferentially form torus type of knots provided a sensitive gauge to evaluate various models of DNA arrangement in phage heads. Only models resulting in a preponderance of torus knots could be considered as close to reality. Recent studies revealed that experimentally observed enrichment of torus knots can be qualitatively reproduced in numerical simulations that include a potential inducing nematic arrangement of tightly packed DNA molecules within phage capsids.

Weak-to-strong confinement transition of semi-flexible macromolecules in slit and in channel.

We compare confinement of stiff macromolecule in channel and in slit. Whereas in the channel a distinct and established transition exists, we elucidate here an ongoing controversy reported from previous experiment and simulation on existence of such transition in the slit. Our extensive molecular simulations in both geometries show only a very weak conformational crossover between moderate and strong confinements in slit in the same range of confinements where the distinct transition in channel is observed.

Persistence length of DNA molecules confined in nanochannels.

The influence of confinement on the persistence length of dsDNA molecules under a high ionic strength environment was explored by coarse-grained Monte Carlo simulations in channels of different profiles. It was found that under confinement three definitions of the persistence length of DNA molecules were not equivalent and represented different properties. In case of the global quantities, the projection and the WLC persistence lengths, the apparent values up to several hundred nanometres are observed for DNA confined in narrow channels.

Channel confinement of flexible and semiflexible macromolecules.

We compare in detail the channel confinement of flexible and semiflexible chains over a broad range of confinements and chain lengths using molecular simulations. Flexible and semiflexible chains differ over the regimes involved under confinement. For the stiff chain we confirm a transition between strong and weak confinement at the tube diameter approximately equal to the chain persistence length.

Chain extension of DNA confined in channels.

The mechanism of DNA elongation in nanochannels was explored by Monte Carlo simulations as a function of the channel dimension D, DNA length, and stiffness. Simulations were based on the bead-spring model, representing double-stranded DNA chains of moderate length at a high salt concentration. As a rule, the channel-induced elongation profiles of R( parallel) vs D from the simulations were in qualitative agreement with those from microfluidic measurements of DNA.

Energy-driven asymmetric partitioning of a semiflexible polymer between interconnected cavities.

The distribution of a semiflexible chain in the volume of two interconnected spherical cavities of equal size has been investigated by using Monte Carlo simulations. The chain possessed an extension exceeding that of the cavity, leading to large probabilities of translocated states despite the entropic penalty of passing the narrow passage. Furthermore, an asymmetric state with unequal subchain lengths in the two cavities was more favorable than the symmetric state.

Persistence lengths and structure factors of wormlike polymers under confinement.

The behavior of semiflexible chains modeling wormlike polymers such as DNA and actin in confined spaces was explored by coarse-grained Monte Carlo simulations. The persistence length P, mean end-to-end distance R2, mean radius of gyration Rg2, and the size ratio R2/Rg2 were computed for chains in slits, cylinders, and spheres. It was found that the intrinsic persistence length of a free chain undergoes on confinement substantial alteration into the apparent persistence length.